Isotopic fractionation is the basis of tracing the water cycle using hydrogen and oxygen isotopes. Isotopic fractionation factors in water evaporating from free water bodies are mainly affected by temperature and relative humidity, and vary significantly with these atmospheric factors over the course of a day. The evaporation rate (E) can reveal the effects of atmospheric factors. Therefore, there should be a certain functional relationship between isotopic fractionation factors and E. An average isotopic fractionation factor (α*) was defined to describe isotopic differences between vapor and liquid phases in evaporation with time intervals of days. The relationship between α* and E based on the isotopic mass balance was investigated through an evaporation pan experiment with no inflow. The experimental results showed that the isotopic compositions of residual water were more enriched with time; α* was affected by air temperature, relative humidity, and other atmospheric factors, and had a strong functional relation with E. The values of α* can be easily calculated with the known values of E, the initial volume of water in the pan, and isotopic compositions of residual water.